One idea could be that Naruto discovers he has a special power that only activates at night. For example, he might be able to communicate with nocturnal animals and they help him in his ninja missions. Another could be that at night, Naruto's appearance changes in a way that gives him an edge in stealth, like his hair turns black to blend in with the darkness better.
In this fanfic, a possible plot could be that Naruto, now a woman, decides to use her new form to her advantage in undercover missions. She could infiltrate enemy groups more easily as a woman. Also, her bond with her sensei Kakashi could change. Kakashi might have to adjust his training methods for her, and Naruto could learn different aspects of ninjutsu and strategy that were more suited to her new gender.
One idea could be to have Naruto characters participate in the Holy Grail War. For example, Naruto himself could be a Servant, perhaps with his chakra being a unique form of mana. His skills like the Rasengan could be reimagined as powerful Noble Phantasms. Another idea is to put the Fate Stay Night characters in the Naruto world. They might have to deal with things like ninja clans and the politics of the hidden villages while also trying to find a way back to their own world.
In a fanfic, Naruto turning into a Pokemon might also lead to some comical situations. Imagine Naruto, now as a Pokemon, trying to communicate with his friends in Konoha. He might have to use Pokemon sounds and gestures at first, causing a lot of confusion among his comrades. But eventually, they figure out a way to understand him, and it becomes a fun adventure for everyone.
One idea could be to explore what happens when a new and very strange artifact is added to the museum. Maybe it has some sort of magical power that affects all the exhibits in unexpected ways. For example, it could make the dinosaurs start speaking in modern languages or the statues come to life with different personalities than before.
Well, a cool plotline could be Naruto using her new female form to her advantage in missions. Maybe she can infiltrate places more easily as a girl. Also, there could be a plot where Naruto has to hide the fact that she was once a boy from some new characters she meets. This could lead to some really funny or tense situations as she tries to keep her secret while still being herself.
A plot could be that Mordred is summoned by a powerful ninja as a last - ditch effort to fight against an ancient evil that has emerged in the Naruto world. This evil has powers similar to some of the powerful Servants in Fate Stay Night, so Mordred's expertise is needed.
One idea could be a time - travel fanfic where Naruto or Sasuke go back in time and try to change certain events. This would allow for a lot of creative storytelling as they interact with their younger selves and try to prevent future tragedies.
One idea could be to create an alternate universe where Naruto has a different elemental affinity from the start. For example, instead of wind, he has lightning. Another could be a fanfic focused on the relationships between the characters outside of the main plot, like how Sakura and Ino rekindle their friendship in a more in - depth way. Or you could write about Naruto's training journey with a different mentor, say Jiraiya's long - lost brother who has a completely different teaching style.
One idea could be a fanfic where Naruto travels to a different dimension where the Akatsuki are the heroes. Another could be a story about Naruto's kids growing up in a world where there's a new threat that they have to face without their parents' immediate help. And a third idea is a fanfic where Naruto discovers a hidden bloodline within himself that gives him unique powers.
Perhaps it could be about self - discovery. The characters who have been transformed now have to figure out this new identity as a girl. They might struggle with different cultural expectations in the Naruto world that are placed on females. This could lead to interesting character development.